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In this article the most fundamental decomposition-based optimization method - block coordinate search, based on the sequential decomposition of problems in subproblems - and building performance simulation programs are used to reason about…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
We present a detailed study of the performance and reliability of design procedures based on energy minimization. The analysis is carried out for model proteins where exact results can be obtained through exhaustive enumeration. The…
In topology optimization of compliant mechanisms, the specific placement of boundary conditions strongly affects the resulting material distribution and performance of the design. At the same time, the most effective locations of the loads…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Distributed optimization algorithms are essential for training machine learning models on very large-scale datasets. However, they often suffer from communication bottlenecks. Confronting this issue, a communication-efficient primal-dual…
Proteins in photosynthetic membranes can organize into patterned arrays that span the membrane's lateral size. Attractions between proteins in different layers of a membrane stack can play a key role in this ordering, as was suggested by…
Engineering new molecules with desirable functions and properties has the potential to extend our ability to engineer proteins beyond what nature has so far evolved. Advances in the so-called "de novo" design problem have recently been…
Dynamic rupture propagation along an interface between two different elastic solids under shear dominated loading is studied numerically by a 2-D lattice particle model (LPM). The configuration of the lattice particle model consists of two…
We propose a criterion for optimal parameter selection in coarse-grained models of proteins, and develop a refined elastic network model (ENM) of bovine trypsinogen. The unimodal density-of-states distribution of the trypsinogen ENM…
We present two simplified models of protein dynamics based on Langevin's equation of motion in a viscous medium. We explore the effect of the potential energy function's symmetry on the kinetics and thermodynamics of simulated folding. We…
Consistently atomistic understanding of the mechanism behind the intriguing behavior of low-dimensional systems including monatomic chains, hollow tubes, surface skins, nanocavities, nanowires, and nanograins has long been a high challenge.…
We theoretically analyze the experimental observations of a spectral line collapse in a metamaterial array of asymmetric split ring resonators [Fedotov et al., Phys. Rev. Lett. 104, 223901 (2010)]. We show that the ensemble of…
Materials that respond to external stimuli by expanding or contracting provide a transduction route that integrates sensing and actuation powered directly by the stimuli. This motivates us to build colloidal scale robots using these…
Nature-inspired stochastic metamaterials with disordered and multiscale architectures have shown great promise towards extraordinary functionalities, including high mechanical resilience, stress modulation and biased stiffness…
While the forward and backward modeling of the process-structure-property chain has received a lot of attention from the materials community, fewer efforts have taken into consideration uncertainties. Those arise from a multitude of sources…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms…
Shells, i.e., objects made of a thin layer of material following a surface, are among the most common structures in use. They are highly efficient, in terms of material required to maintain strength, but also prone to deformation and…